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Updated: Mar 18, 2026

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
Published on: December 16, 2013
Thermodynamically-Weighted Conformational Ensemble of Cyclic RGD Peptidomimetics from NOE Data
F Vasile1, M Civera1, L Belvisi1
1Department of Chemistry, Università degli Studi di Milano , via Golgi 19, 20133 Milano, Italy.
Abstract:
In the case of flexible molecules, the standard approach of transforming NOE intensities into spatial restraints and of building conformational models minimizing these restraints greatly neglects the richness of molecular conformations. Making use of NOE intensities measured in triplicate and of an iterative molecular-dynamics scheme, we optimized a force field to generate a set of conformations whose ensemble is compatible with the experimental data, and is weighted according to the Boltzmann distribution. This scheme is applied to two cyclic peptidomimetic ligands of integrins. Their difference in binding affinity is recapitulated in terms of their difference in conformational fluctuations.
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